Rapid innovation in ChIP-seq peak-calling algorithms is outdistancing benchmarking efforts

Introduction into the analysis of high-throughput-sequencing based epigenome data

(2010) M. Huss   BRIEFINGS IN BIOINFORMATICS

De novo motif identification improves the accuracy of predicting transcription factor binding sites in ChIP-Seq data analysis

(2010) Valentina Boeva et al.   NUCLEIC ACIDS RESEARCH

Towards a Rigorous Assessment of Systems Biology Models: The DREAM3 Challenges

(2010) Robert J. Prill et al.   PLoS One

MER41 Repeat Sequences Contain Inducible STAT1 Binding Sites

(2010) Christoph D. Schmid et al.   PLoS One

Evaluation of Algorithm Performance in ChIP-Seq Peak Detection

(2010) Elizabeth G. Wilbanks et al.   PLoS One

BayesPeak: Bayesian analysis of ChIP-seq data

(2009) Christiana Spyrou et al.   BMC BIOINFORMATICS

A practical comparison of methods for detecting transcription factor binding sites in ChIP-seq experiments

(2009) Teemu D Laajala et al.   BMC GENOMICS

Bioinformatics approaches for genomics and post genomics applications of next-generation sequencing

(2009) D. S. Horner et al.   BRIEFINGS IN BIOINFORMATICS

ChIP-seq accurately predicts tissue-specific activity of enhancers

(2009) Axel Visel et al.   NATURE

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls

(2009) Joel Rozowsky et al.   NATURE BIOTECHNOLOGY

Computation for ChIP-seq and RNA-seq studies

(2009) Shirley Pepke et al.   NATURE METHODS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Sole-Search: an integrated analysis program for peak detection and functional annotation using ChIP-seq data

(2009) Kimberly R. Blahnik et al.   NUCLEIC ACIDS RESEARCH

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

(2009) Elodie Portales-Casamar et al.   NUCLEIC ACIDS RESEARCH

Inherent Signals in Sequencing-Based Chromatin-ImmunoPrecipitation Control Libraries

(2009) Vinsensius B. Vega et al.   PLoS One

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE

A blind deconvolution approach to high-resolution mapping of transcription factor binding sites from ChIP-seq data

(2009) Desmond S Lun et al.   GENOME BIOLOGY

GeneTrack--a genomic data processing and visualization framework

(2008) I. Albert et al.   BIOINFORMATICS

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

(2008) A. P. Fejes et al.   BIOINFORMATICS

Empirical methods for controlling false positives and estimating confidence in ChIP-Seq peaks

(2008) David A Nix et al.   BMC BIOINFORMATICS

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

(2008) D. S. Johnson et al.   GENOME RESEARCH

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data

(2008) R. Jothi et al.   NUCLEIC ACIDS RESEARCH

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY